PPT-Microbial Genome Annotation

Nikos Kyrpides DOE Joint Genome institute Two main goals of genome analysis Evolutionary analysis How does an organism compare to the rest Metabolic reconstruction What can an organism do and how. Denovo genome Denovo genome outline outline novogenome from contigs from assembled contigs annotation Denovo genome Denovo genome Reads contig Gene Gene Annotation Gene Annotation Forgene BCB 660. October 20, 2011. From Carson Holt. Annotations. Automated. Ab. initio. (based on genomic sequence alone). Involves comparisons to known proteins (BLAST similarity). Sequence motifs such as start/stop . Venter et. al (2004). Presented by. Ken . Vittayarukskul. Steven S. White.. Context of the Problem . Evolutionary history is directly tied to microbial genetics. Little is known. Until recently, microbial diversity was measured by PCR amplification and sequencing of only ribosomal genes. Nikos. . Kyrpides. Genome . Biology . Program (GBP). DOE Joint Genome institute. IMG. Genes. Genomes. Functions. Metadata. Clusters. SNPs. Proteomics. Regulons. Transcriptomes. IMG Systems Data Types. Bas E. Dutilh. March 4. th. 2013. Protein function. Phenotypic. . function. E.g. . apoptosis. GO: . Biological. . process. Cellular. . function. E.g. . ribosome. GO: . Cellular. component. Molecular. Daniel Standage. Biology Department. Indiana University. An-no-ta-. tion. . \ˌa. -. nə. -ˈ. tā-. shən. \. A critical or explanatory note or body of notes added to a text. The act of annotating. Last Updated: 12/26/2021. Wilson Leung and Chris Shaffer. Agenda. Overview of the GEP annotation project. GEP annotation strategy. Types of evidence. Analysis tools. Web databases. Annotation of a single isoform (walkthrough). “. User facility. providing high-throughput DNA sequencing & analysis in support of DOE missions in alternative . energy. , . carbon cycling . & . bioremediation. .”. Opened in 1999. ~240 UC Employees. Loren Hauser. Miriam Land. Yun-Juan Chang. Frank Larimer. Doug Hyatt. Cynthia Jeffries. NEB Educational Support. 2. http://www.neb.com/nebecomm/course_support.asp?. Why study Computational Biology. . immunoregulatory. microbial . product. Matthew Rhodes and Catherine . Lozupone. University of Colorado, Denver. Rocky Mountain Bioinformatics Conference. December 11. th. 2014. Mazmanian. and Kasper . October 20, 2011. From Carson Holt. Annotations. Automated. Ab. initio. (based on genomic sequence alone). Involves comparisons to known proteins (BLAST similarity). Sequence motifs such as start/stop . HHMI Logistics. . Name badges must be worn at all times. Restrooms. No roaming through the building. Questions? – Ask . us. Refreshments . (keep to the schedule). Technology. Live Streaming. The microphones. a . Tool for Online Annotation and . Curation. Dorrie Main, Taein Lee, Ping . Zheng. , Sook Jung, Stephen P. Ficklin, Jodi Humann, . Jill . Wegrzyn.  and David Neale. What is . GenSAS. ?. It is a web-based . However, genomes are large and complex and visualizing this information is not easy. You need to imagine that the raw annotation information, by itself, can be contained in a text file, which could include positional information (coordinates relative to the reference genome) and different features (e.g. annotation type – gene, mRNA, intron/exon, variant, UTR, etc.).